Thanks for explaining more.
Please try the following to see if it helps:
1. Load the FBX or the character in a T-Pose (if prompted to use a pre-set say no).
2. In 3DXchange 7 choose "Convert To Non-Standard" from the Modify Panel.
3. Apply the Maya Human IK pre-set from the dropdown. The indicator light should turn green to show the bones have been mapped correctly.
4. Check "Active" and try some preview animations to make sure everything is ok.
5. If it is click "Convert".
6. Now in the Animation (M) section of the Modify Panel choose "Import".
7. Now select the other animations for this character which should be correctly applied and added to the animation list.
8. The character should now be ready to send to iClone.
Do give this a try and see if it helps.